It's dependant on the offset and width of the wheel.

I think you're better off with the way it is right now. If it's flush, you are gonna rub, it's going to throw more water, mud, etc on the side of your car.

And as far as alignment goes...you don't need one if all you did was put new wheels on. If you haven't had alignment since the car was dropped, then you should. But it won't affect how the wheels sit.